Squeezing DNA by trying to stretch it out

It turns out that, sometimes, when you apply an electric field to DNA, it …

Manipulating DNA is now a cornerstone of science. We are able to synthesize DNA strands with a given sequence, we can move it, purify it, measure its length, stitch it together with other DNA molecules, and a whole lot more. Some of our techniques work better on populations of DNA strands rather than single molecules, but, it is still amazing to me that we have such control.

What is more amazing is to have that level of control and then discover something completely new about DNA. In this case, it was common knowledge that DNA, which is a highly charged molecule, will stretch out in the presence of an electric field. But, umm, it seems that this isn't always true.

Funnily enough, I have a rather embarrassing relationship to this research. A long time ago, I wanted to develop a new, and relatively quick way to discover how long the DNA strands were in a mixed sample sample. One of the ideas involved using AC electric fields that scanned through different frequencies. The idea was that DNA would extend in response to the electric field until the frequency was too high, whereupon the DNA would no longer extend.

We made a model of DNA and, hey, it worked—the idea was good. Except that there was a bug in the code. When removed, it still sort-of worked. When we attempted to publish the model—the experiment never worked to our satisfaction—we discovered that we really didn't know much about DNA. And this painful discovery has stood me in good stead ever since.

The cool thing about this recent bit of work is that it shows that not only was I wrong, I was so wrong that, should the experiments have worked, it would have made it into Physical Review Letters. Because it turns out that, for a critical frequency, DNA strands compress in the presence of AC electric fields.

The basic experiment is, at first glance, fairly simple. A microfluidic device has DNA flowing along its channels. These channels are narrow enough that the DNA is somewhat stretched out by restriction from the walls. The researchers then applied AC electric fields in the frequency range of around 300-700Hz. For the length of the DNA strands that they used, this frequency is high enough that the molecule as a whole has no time to respond. In effect, current models predict that the researchers should have observed nothing.

Indeed, when the electric field amplitude is low, the DNA really doesn't respond. But, for a given frequency, there appears to be a critical electric field amplitude, above which the DNA rapidly collapses into a tight ball. (Actually, in their data, the balls are elongated because the DNA strands are traveling down a microfluidic channel during the measurement.) Further investigation revealed that the threshold voltage increased with frequency, and that the final compression depended on how large the applied field was. That is, once above the threshold, the degree of compression increased with strength of the applied field.

This almost certainly left the researchers befuddled. No one expected this at all and there are no DNA models that actually predict that it will compress in a given AC electric field. Zhou and co-workers propose a pair of mechanisms that would explain the behavior but, as they note, their models only explain the general trend, not the actual performance they saw.

One possible mechanism is due to the charge distribution in hairpin sections of DNA, where a single strand folds back and base pairs with itself. The idea is that, when a filed is applied, the ions in the surrounding medium move along the DNA backbone, shielding the DNA's charge from the surrounding fluid—from a distance, the whole lot looks neutral. When DNA coils form a hairpin, it introduces higher spatial frequency components into the path that the ion must travel and, for the ions to remain mobile, they have to posses these frequency components.

The high frequency AC field jiggles them about vigorously, providing them with the necessary range of different motions so that they can efficiently traverse to the hairpin. As a result, charge gathers at the curvy sections of the DNA. Nearby curvy sections will sense each other and drive the like-charged ions to opposite sides of the curve, making them attractive to each other. These then draw into each other, compressing the DNA.

The researchers also proposed a second possible mechanism, based on localized density fluctuations. DNA is a polymer chain, meaning that it is a series of tangled blobs interconnected by relatively straight, low density sections. Neighboring high density sections should have mirror charge distributions, so that they become mutually attractive. But, in this case, the connection between the charge distribution and the electric field frequency is less clear. I suspect that, in fact, the two mechanisms are part of the same thing, where the hairpin forming regions compress the blobs into a high density block containing lots of ions. These then form mirror charge distributions as they interact with neighboring blocks, allowing them to compress and then pull the blobs into each other.

This is a really cool piece of research—combining, as it does, something we thought we understood really well with very surprising experimental results that tell us we didn't understand it quite as well as we thought. I look forward to seeing the development of predictive models that explain this. And, I expect that this will find its place in the toolbox of DNA manipulation.

Chris Lee / Chris writes for Ars Technica's science section. A physicist by day and science writer by night, he specializes in quantum physics and optics. He lives and works in Eindhoven, the Netherlands.